<div><div>Hi all,</div><div><br></div><div>I will highly appreciate your help
to resolve the following bugs encountered during running phenix.refine on GUI
as well as on command lines.</div><div><br></div><div>My version of Phenix and
platform are: </div><div>PHENIX: Python-based Hierarchical ENvironment for
Integrated Xtallography</div><div> Version:
1.4</div><div> Release tag: 3</div><div> cctbx tag:
2008_12_07_1353</div><div> Platform: mac-intel-osx
osx-10.5.8</div><div><br></div><div><br></div><div><b>The error encountered
using phenix refinement GUI (phenix.refine_gui) is as
follows:</b></div><div><br></div><div>A Python error was detected. This
is almost certainly a bug; please send an email containing this message to
phenixbb@phenix-online.org so we can fix it.
Thanks!</div><div>RuntimeError : min() argument is an empty
array</div><div>Traceback:</div><div>Traceback (most recent call
last):</div><div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Base.py", line 274, in
OnBrowse</div><div>
self.file_text_field.SetValue(new_path)</div><div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Controls.py", line 974, in
SetValue</div><div>
self.phil_handler.propagate_update(self.phil_def_name,
new_value)</div><div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/PhilInterfaceHandler.py", line 103, in
propagate_update</div><div>
self._update_handlers[def_name](self, def_name,
value)</div><div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Extensions.py", line 28, in
extract_xray_neutron_params</div><div> phil_def_name =
phil_object_name)</div><div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 155, in
__init__</div><div> self.load_reflection_file(file_name,
phil_def_name)</div><div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 159, in
load_reflection_file</div><div> self.hkl_server =
self.hkl_handler.add_hkl_file(file_name,
phil_def_name)</div><div> File
"/usr/local/phenix-1.4-3/phenix/wxGUI2/Reflections.py", line 66, in
add_hkl_file</div><div>
err=sys.stderr)</div><div> File
"/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in
__init__</div><div>
force_symmetry=self.force_symmetry))</div><div> File
"/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in
as_miller_arrays</div><div>
base_array_info=base_array_info)</div><div> File
"/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in
as_miller_arrays</div><div> and
flex.min(column_group.sigmas()) >
0):</div><div><br></div><div><br></div><div><b>The error encountered using
phenix refinement on command line (phenix.refine coordinate.pdb reflection.mtz)
is as follows:</b></div><div><br></div><div>Traceback (most recent call
last):</div><div> File
"/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in
<module></div><div>
command_line.run(command_name="phenix.refine",
args=sys.argv[1:])</div><div> File
"/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 68, in
run</div><div> log=log)</div><div> File
"/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 231,
in __init__</div><div> reflection_file_server =
self.reflection_file_server()</div><div> File
"/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 566,
in reflection_file_server</div><div>
err=self.log)</div><div> File
"/usr/local/phenix-1.4-3/iotbx/reflection_file_utils.py", line 393, in
__init__</div><div>
force_symmetry=self.force_symmetry))</div><div> File
"/usr/local/phenix-1.4-3/iotbx/reflection_file_reader.py", line 197, in
as_miller_arrays</div><div>
base_array_info=base_array_info)</div><div> File
"/usr/local/phenix-1.4-3/iotbx/mtz/__init__.py", line 434, in
as_miller_arrays</div><div> and
flex.min(column_group.sigmas()) > 0):</div><div>RuntimeError: min() argument
is an empty array</div><div><br></div><div>N.B. Earlier, I had encountered the
similar error (using command line) using PHENIX version 1.3 on the same
platform.</div><div><br></div><div>Thanks in
advance.</div><div><br></div><div>Regards,</div><div><br></div><div>Ravi</div><div><br></div><br>Ravindra D. Makde, PhD<br>Postdoctoral fellow, Tan lab,<br>The Department of Biochemistry and Molecular Biology,<br>The Pennsylvania State University,<br>University Park, PA 16802<br>USA<br><br><br></div>